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As Li-on pointed out, the final choice of the game was likely a final appeal by the Reapers to convert Shepherd to their side. Option 1: Control the Reapers (yeah right) Option 2: Synthesize with the Reapers (like the Protheans) or Option 3: Destroy the Reapers

The indoctrination theory wraps this up fairly well by stating most of the events that happen after Shepherd is hit by Harbinger's red beam are in fact an inner conflict in Shepherd's mind. This explains why Anderson and Illusive Man are conveniently waiting for him on the Citadel and the Gray Sweatshirt Kid (who was likely a hallucination the whole time) presents himself as a Godlike being, the Catalyst, and in control of the Reapers. All 3 games have focused very closely on indoctrination with Saren, Illusive Man, Harbinger, Rachni Queen, the Geth etc. There's even a codec that warns specifically about the dangers of indoctrination and talks about symptoms that Shepherd displays in this game...

The video goes into even more depth but I think most of the arguments that I've read trying to contradict the indoctrination theory fail to answer the questions presented at the end of the youtube video that indoctrination theory resolves. While I don't think the ending completely resolves the game, I'm at least happy that the game now makes sense. For me it's like the ending of BSG or Brazil: the reality of your situation is grim but there's beauty in accepting defeat and giving up on the hope of a brighter future.

Anyway, what opinions does everyone else have on the whole indoctrination theory thing?

I agree with what's called indoctrination theory (which was put forward by reasonably sounding folks and not the angry internet mob, thus has much less publicity). As I pointed out in the other ME3 thread, I thought right away that the whole sequence on the citadel was a hallucination (respectively reaper indoctrination). TIM and Anderson are manifestations of reaper control (TIM) and Shepards will to resist (Anderson). The child simply lies to you and contradicts too much we heard during the course of all 3 games. Being the lovely Renegade I've been throughout all 3 games I was of course going for the destroy ending.

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Originally Posted by Havblue

For me it's like the ending of BSG or Brazil: the reality of your situation is grim but there's beauty in accepting defeat and giving up on the hope of a brighter future.

I had the same feeling, immediately thought about the end of BSG once I was through. A lot of fans seem to be up in arms because it actually is an ending. The Mass Effect Universe we travelled through in these 3 games will not be the same again. I actually like having an end of a story for a change.

It's surprising how much of the game fits into place when you take into account how important the whole subject of indoctrination is. The whole game I was wondering what Ashley's problem was. Her first reaction to seeing a Cerberus soldier turned into a husk was concern and distrust for Shepherd. As shocking as it sounds, she was right to be concerned.

Bioware obviously has DLC in production to help resolve the ending. The paragon decision will be if they release it for free. The renegade decision will be you can beat the Reapers once and for all for only $9.99. And if you thought people were angry already wait for their reaction when they find out they need to pay more for the real ending...

It's surprising how much of the game fits into place when you take into account how important the whole subject of indoctrination is.

This idea hit me the first time during the mission against Cerberus where some vid-logs reveal just how bad Shepards condition was when project Lazarus started. When it was implied that they have used reaper-tech to bring Shepard back to life was when the alarmbells really rang. Miranda can tell me as long as she wants that there is no control chip in Shepard, the fact remains he was dead and that he's alive again is way beyond what the scientists could have achieved without some reaper blueprints.

I started a Mass Effect 1 campaign now and suddenly I see Saren's betrayal in a new light. A lot of things that are mentioned in ME1 I see now in a different light. Funny how things the Rachni-Queen in part 1 says responds to things I noticed in Shepards Nightmares. They really did plan it out as a trilogy, which is one more reason why I think this ending was not 'just an accident'.

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The whole game I was wondering what Ashley's problem was.

Hah, I was quite annoyed about her reaction on Mars. But yes, she probably was right all along: Cerberus cannot be trusted and Shepard was a fool thinking he could use TIM to his advantage.

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The paragon decision will be if they release it for free. The renegade decision will be you can beat the Reapers once and for all for only $9.99. And if you thought people were angry already wait for their reaction when they find out they need to pay more for the real ending...

lol I can see how an EA manager is doing a renegade-interrupt when a rogue coworker tries to upload the dlc for free

The 'you can buy dlc now' at the end of the credits was what pretty much confirmed for me right away that there's something still coming. The thought of paying 10$ extra to get the real ending annoys me. I didn't buy the day1 dlc because I don't like how the ME franchise gets milked (respectively the fans) and because the ME2 dlc I bought was rarely worth the money (with exception of Shadow Broker's, which was only slightly overpriced). To get the full ending and closure for the ME storyline I have to dish out for dlc? Then I can safely say ME3 was the last Bioware game I bought at full price. I still love their games, but as a consumer I feel cheated. Imagine you go for the latest movie and after 2 hours the credits roll but you can see the real ending for just 20% extra...

Going out on a limb here, but I think the surprise ending is that Mass Effect is actually a prequel to Assassin's Creed - look at how the Starchild is dressed: he is clearly a young Desmond Miles. Which is also why he's so annoying.

Seriously, though, I buy the indoctrination ending. Even if it's not the developer's intent, I'd rather stick with this interpretation.

If it is the developer's interpretation, I think it's one of the best game endings ever - the paragon and renegade colours are reversed, no overt revalation - basically, the player is indoctrinated by the conventions of the gameworld! Genius!